Introduction

Thanks for using LncPipe! LncPipe is a nextflow-based pipeline which collected several popular tools and in-house scripts so as to identifiy and analyze novel lncRNAs from raw RNA sequencing data. As we known, identification and profiling of lncRNAs is a fundamental step to advance our knowledge on their function and regulatory mechanisms. We thus presents LncPipe to facilite the relanvet research on LncRNA discovery and annotation. This report was automaticly generated by pipeline and consist of several sections as follows:

1. Raw fastq quallity control result soft links by FastQC.(Only available when fastQC step was not skipped by --skip_QC)
2. Reads alignment summary. Since the intial mapping step was carried out by STAR, we summarized the basic information that can help control the library quanlity of each samples.
3. Novel lncRNAs basic charateristics such length distribution, exon number, coding potiential and classifications.
4. Differential expression analysis if design file was feed. Abandunce of each transcript was assessed and compared between conditions. We also provide exploration analysis like PCA and clustering to help check the experimental design.
5. Comparison analysis was also performed between coding gene, known lncRNA and novel lncRNAs

Nextflow running parameters

Reporter runing parameters

Quality control

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STAR log plot

STAR log table

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HISAT percentage plot

HISAT log table

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CDF against CPAT

CPAT table

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Table

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Differential expressed lncRNAs table

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